- Acting for Two: Yuuto Kazama voices both Zero and Copy X, ironically enough.
- Flip-Flop of God: The fate of the Four Guardians during/after Zero 3. U-CAPCOM's response to a fan letter about the matter (see here) claimed they were probably off continuing the fight against Dr. Weil in some unknown place, while the Mega Man Zero Complete Works artbook claimed they died in Omega's boss explosion, shielding Zero from the brunt of the explosion. Most recently, in the MM25: Mega Man & Mega Man X Complete Works Q&A session, it was claimed that Neo Arcadia has no records of further activity from them and in-story they're considered deceased, but they could still be alive beyond its sensors.
- Manual Misprint: For one reason or another, the Official Complete Works lists some of the game's Mutos Reploids as "your Resistance allies."
- No Export for You: The e-Reader bonus content for the original GBA Zero 3, though this was averted for the Zero Collection and Zero/ZX Legacy Collection re-releases). It can be nevertheless be enabled in non-Japanese versions via cheat codes, complete with English text.
- The Other Darrin: Both Zero and X have new voice actors that were never used in the Mega Man X series; Zero is played by Ryōtarō Okiayu in X and Yuuto Kazama in Zero, while X had been played by Showtaro Morikubo up until X7 and is played by Takahiro Mizushima in Zero. Interestingly, instead of adopting the Zero series' actors, the X series continued using Okiayu for Zero and diverged into a new example of The Other Darrin for X by introducing Takahiro Sakurai to the role (from Command Mission onward).
- Post-Script Season: The series was meant to end with Zero 3, as evidenced by resolving the Dark Elf storyline, giving X his eternal rest, bookending with the lab ruins, etc. and developer interviews. Of course, we got Zero 4, which turned a Post-Script Season into a proper Grand Finale. Strangely, the fates of the three living Guardians after Omega's death were completely ignored until the Zero Complete Works, which says they died in Omega's explosive death throes. The fourth game doesn't so much as mention them.
- Urban Legend of Zelda: It's theorized that Dr. Weil was originally going to be Dr. Wily, but the continuation of the Mega Man X series cancelled that in the event that the subplot of Wily being Zero's creator got resolved there. This is supported by their similar sounding names, Weil's knowledge on Zero's design, and the implication that Dr. Wily was still alive throughout the X games (particularly in Mega Man X5, the original finale to the X series, though Serges and Isoc were also implied to be robotic avatars of Wily), but was never confronted.
- What Could Have Been:
- The original premise had the real X as the antagonist, but this was changed late into development to make him a troubled replica called Copy X instead.
- Some very early concept art depicted Pantheons as Reploids brainwashed by a face-hugging helmet.
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